Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81368	0.162
27DAP/17DAP	1.00388	0.952
39DAP/27DAP	1.14535	0.981
41DAP/39DAP	0.97354	0.752
42DAP/41DAP	0.78585	0.774
43DAP/42DAP	0.84575	0.671
47DAP/43DAP	0.91369	0.699
52DAP/47DAP	1.0586	0.999
57DAP/52DAP	0.85928	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00222	0.806
17DAP/reference	0.96725	0.567
27DAP/reference	0.87447	0.095
39DAP/reference	0.81669	0.039
41DAP/reference	0.82747	0.039
42DAP/reference	0.86718	0.014
43DAP/reference	0.86721	0.031
47DAP/reference	0.85531	0.006
52DAP/reference	0.74133	0.026
57DAP/reference	0.88845	0.096

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9525	0.595
27DAP/17DAP	1.03247	0.954
39DAP/27DAP	0.86929	0.173
41DAP/39DAP	0.86193	0.201
42DAP/41DAP	1.00177	0.902
43DAP/42DAP	0.97602	0.774
47DAP/43DAP	0.94688	0.637
52DAP/47DAP	0.90332	0.382
57DAP/52DAP	0.93866	0.56
57DAP/7DAP	1.06656	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96854	0.55
17DAP/reference	0.98828	0.518
27DAP/reference	1.01445	1
39DAP/reference	0.81327	0.018
41DAP/reference	0.87742	0.086
42DAP/reference	0.89923	0.09
43DAP/reference	0.77256	0.012
47DAP/reference	0.85444	0.222
52DAP/reference	0.68849	0.017
57DAP/reference	0.8001	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13916	0.072
17DAP/reference	1.29641	0.015
27DAP/reference	1.02358	0.948
39DAP/reference	0.86476	0.04
41DAP/reference	0.94874	0.141
42DAP/reference	0.94882	0.289
43DAP/reference	1.14106	0.356
47DAP/reference	0.92058	0.123
52DAP/reference	0.77742	0.023
57DAP/reference	0.89126	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94046	0.362
17DAP/reference	1.00168	0.9
27DAP/reference	1.04795	0.777
39DAP/reference	0.95219	0.36
41DAP/reference	1.01454	1
42DAP/reference	1.00968	1
43DAP/reference	0.71013	0.023
47DAP/reference	0.71721	0.004
52DAP/reference	1.05059	0.888
57DAP/reference	0.70027	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08754	1
26DAP/20DAP	1.18493	0.449
34DAP/26DAP	0.8634	0.539
51DAP/34DAP	1.18021	0.314
52DAP/51DAP	0.91185	1
53DAP/52DAP	0.88408	0.365
55DAP/53DAP	0.81812	0.067
57DAP/55DAP	0.99057	0.923
62DAP/57DAP	1.16684	0.678
68DAP/62DAP	1.1429	0.869
68DAP/14DAP	0.81327	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69862	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.27654	0.058
Mature Green Tomato/Ripe Tomato	2.03459	0.017
Immature Eggplant/Mature Eggplant	0.77569	0.071
Ripe Pepper/Ripe Tomato	0.99157	1
Mature Eggplant/Ripe Tomato	2.31161	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00008	1
1-1-2/M82	0.92715	1
12-2/M82	1.21798	1
12-4/M82	1.02134	1
1-3/M82	0.86297
2-1-1/M82	0.794
2-1/M82	1.05071
2-6/M82	0.93622	1
3-2/M82	1.10606
4-1-1/M82	0.84142	1
4-1/M82	0.93299	1
4-3-2/M82	0.72854	0.487
4-3/M82	0.59126	0.475
5-3/M82	1.0878	0.496
6-2/M82	0.98662	1
6-3/M82	1.31777
7-1/M82	N/A	N/A
7-2/M82	1.00581	1
9-3-2/M82	0.99168	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.65633	0.247
IL2-6/WTpooled	1.07901
IL7-5/WTpooled	1.55418	1
IL7-3/WTpooled	0.78942	1
IL12-4/WTpooled	1.01134	0.891
IL1-4/WTpooled	0.93598	0.834
WT/WTpooled	1.00037	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.04017	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00618	0.921
DC3000/delta hrp 6h	1.006	0.95
DC3000/delta hrp 12h	0.92492	1
DC3000/delta hrp 24h	0.93816	0.585

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.93888	0.568
DC3000 delta B/DC3000 delta AB	1.05866	0.771

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93416	1
Exp 36h	0.90183	0.397
Exp 60h	1.01142	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.00561	1
Var 0h	1.42821	1
Var 12h I row2-row1	0.87661	0.418
Var 12h NI row2-row1	1.05479	1
Var 36h I row2-row1	0.87689	0.805
Var 36h NI row2-row1	1.15472	1
Var 60h I row2-row1	0.90683	0.582
Var 60h NI row2-row1	1.03613	1
Time course 0hI-0hNI	0.99538	1
Time course 12hI-12hNI	0.96525	0.628
Time course 36hI-36hNI	0.94493	0.265
Time course 60hI-60hNI	0.56515	0.011

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.13541	0.397
transgenic ySAMdc/azygous control (breaker)	0.85537	0.15
transgenic ySAMdc/azygous control (red)	1.07795	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95556	0.237

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30219	0.222

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17749	0.307
Manapal/WT (break)	1.50942	0.381
Manapal/WT (red)	1.13432	1